AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene034536

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034536.t1 MTR_1g054285 84.804 204 3 4 1 176 1 204 3.37e-114 326
MS.gene034536.t1 MTR_7g093430 54.028 211 61 7 1 176 1 210 7.03e-58 183
MS.gene034536.t1 MTR_4g100550 54.167 120 44 2 59 176 60 170 3.95e-33 119
MS.gene034536.t1 MTR_5g013010 52.672 131 41 4 54 176 69 186 9.97e-33 116
MS.gene034536.t1 MTR_5g013010 53.968 126 37 4 59 176 74 186 1.01e-31 115
MS.gene034536.t1 MTR_2g061030 42.000 250 71 10 1 176 1 250 2.83e-31 115
MS.gene034536.t1 MTR_4g097600 80.000 65 11 1 114 176 113 177 8.50e-29 107
MS.gene034536.t1 MTR_8g006705 54.054 111 45 1 72 176 86 196 6.03e-26 100
MS.gene034536.t1 MTR_5g014890 75.410 61 14 1 117 176 113 173 5.30e-24 95.1
MS.gene034536.t1 MTR_1g017090 46.341 123 51 4 61 176 66 180 2.18e-21 88.6
MS.gene034536.t1 MTR_3g103590 68.333 60 19 0 117 176 136 195 3.34e-21 88.2
MS.gene034536.t1 MTR_4g084750 73.684 57 14 1 121 176 59 115 2.75e-20 84.0
MS.gene034536.t1 MTR_4g126900 69.388 49 15 0 128 176 90 138 3.52e-17 76.3
MS.gene034536.t1 MTR_2g038625 57.353 68 28 1 109 176 66 132 1.75e-16 74.3
MS.gene034536.t1 MTR_2g038580 57.353 68 28 1 109 176 66 132 1.75e-16 74.3
MS.gene034536.t1 MTR_4g107650 50.602 83 37 2 94 176 67 145 2.20e-14 70.1
MS.gene034536.t1 MTR_7g010020 42.391 92 52 1 85 176 40 130 2.97e-14 68.9
MS.gene034536.t1 MTR_8g089895 43.617 94 49 2 83 176 15 104 8.59e-13 65.5
MS.gene034536.t1 MTR_5g038280 48.611 72 34 1 105 176 69 137 1.04e-12 65.1
MS.gene034536.t1 MTR_3g086790 40.196 102 59 2 76 176 10 110 2.46e-12 63.9
MS.gene034536.t1 MTR_6g007647 57.407 54 23 0 123 176 30 83 2.69e-12 63.5
MS.gene034536.t1 MTR_6g007647 57.407 54 23 0 123 176 64 117 3.37e-12 63.5
MS.gene034536.t1 MTR_1g061660 50.909 55 27 0 122 176 55 109 4.01e-12 62.8
MS.gene034536.t1 MTR_8g469430 54.902 51 23 0 126 176 89 139 1.77e-11 61.6
MS.gene034536.t1 MTR_5g039000 50.847 59 29 0 118 176 69 127 2.85e-11 60.8
MS.gene034536.t1 MTR_7g103340 48.276 58 30 0 119 176 56 113 3.54e-11 60.1
MS.gene034536.t1 MTR_6g011610 41.346 104 54 3 79 176 44 146 8.04e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034536.t1 AT5G06710 42.324 241 73 5 1 176 1 240 4.77e-41 139
MS.gene034536.t1 AT5G06710 42.324 241 73 5 1 176 1 240 6.50e-41 140
MS.gene034536.t1 AT5G47370 55.118 127 47 5 59 176 55 180 2.16e-32 117
MS.gene034536.t1 AT4G17460 42.347 196 71 7 3 176 10 185 4.20e-30 111
MS.gene034536.t1 AT3G60390 51.825 137 44 6 59 176 79 212 6.45e-30 111
MS.gene034536.t1 AT4G16780 56.198 121 38 3 59 176 71 179 3.56e-27 103
MS.gene034536.t1 AT2G44910 49.624 133 44 4 60 176 88 213 1.61e-26 102
MS.gene034536.t1 AT2G22800 76.667 60 14 0 117 176 104 163 2.44e-25 99.0
MS.gene034536.t1 AT4G37790 76.667 60 14 0 117 176 117 176 7.28e-25 97.8
MS.gene034536.t1 AT5G06710 36.279 215 71 5 1 150 1 214 3.04e-21 87.4
MS.gene034536.t1 AT5G06710 36.279 215 71 5 1 150 1 214 3.04e-21 87.4
MS.gene034536.t1 AT2G01430 60.294 68 27 0 109 176 122 189 7.00e-21 85.9
MS.gene034536.t1 AT2G01430 60.294 68 27 0 109 176 122 189 2.60e-20 85.5
MS.gene034536.t1 AT1G70920 65.079 63 20 1 116 176 27 89 2.04e-17 75.9
MS.gene034536.t1 AT1G70920 65.079 63 20 1 116 176 57 119 3.48e-17 75.9
MS.gene034536.t1 AT2G36610 45.312 64 27 1 121 176 66 129 3.07e-11 59.7
MS.gene034536.t1 AT3G01470 56.863 51 22 0 126 176 68 118 3.42e-11 60.5

Find 34 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAAAGAGATAGGTAATTT+TGG 0.264059 1.4:+55280420 None:intergenic
AGGAATAACAATGCTGAATA+TGG 0.265099 1.4:-55279714 MS.gene034536:CDS
GGAAGTGATGATGATGAAAA+TGG 0.308043 1.4:-55279651 MS.gene034536:CDS
ATGGAACTTGCTTTGAGCTT+AGG 0.368374 1.4:-55280450 MS.gene034536:CDS
CTTGGTAGTGGATCTTTGTT+GGG 0.374601 1.4:+55280390 None:intergenic
GGAAGAAGGTCTAGTTGAAT+AGG 0.392211 1.4:+55280309 None:intergenic
GTCCTCGTCAAGTTGAAGTT+TGG 0.396562 1.4:-55279411 MS.gene034536:CDS
ACTTGGTAGTGGATCTTTGT+TGG 0.408944 1.4:+55280389 None:intergenic
CTTCGGTCGTCGCCGGAAAA+CGG 0.438226 1.4:+55279808 None:intergenic
TTGCAATGGATTTCAGTATG+AGG 0.457926 1.4:-55279734 MS.gene034536:CDS
TTCTGTGTCACCATTTGCAA+TGG 0.477662 1.4:-55279748 MS.gene034536:CDS
ATACTGAAATCCATTGCAAA+TGG 0.496930 1.4:+55279738 None:intergenic
GATCTAAGAACAGGAGAGAA+AGG 0.503681 1.4:+55280288 None:intergenic
TCGACGTCTTCGGTCGTCGC+CGG 0.507773 1.4:+55279801 None:intergenic
GGTACCGTCGTCGACGTCTT+CGG 0.509499 1.4:+55279791 None:intergenic
AGAAACAAGAGAGAAAATGA+AGG 0.510237 1.4:-55279687 MS.gene034536:CDS
GGTTTGTCAAGAAAAGAGAT+AGG 0.515910 1.4:+55280411 None:intergenic
AATGAAGGTGAAGCTGAAAG+AGG 0.521199 1.4:-55279672 MS.gene034536:CDS
GAAGTGATGATGATGAAAAT+GGG 0.525282 1.4:-55279650 MS.gene034536:CDS
AAATGGTGACACAGAACTGC+TGG 0.531470 1.4:+55279755 None:intergenic
TGTTGGGTTGAGAAGAAACT+TGG 0.533644 1.4:+55280372 None:intergenic
ATGATGAAAATGGGTCAACT+AGG 0.551419 1.4:-55279641 MS.gene034536:CDS
GAACAGGAGAGAAAGGAAGA+AGG 0.553836 1.4:+55280295 None:intergenic
GTTGAGAAGAAACTTGGTAG+TGG 0.575951 1.4:+55280378 None:intergenic
GAAATTTACAGGATTAAGAG+TGG 0.579010 1.4:+55279557 None:intergenic
AGAAGGTCTAGTTGAATAGG+TGG 0.598462 1.4:+55280312 None:intergenic
GGTTTCAAAATAGAAGAGCA+AGG 0.607323 1.4:-55279390 None:intergenic
AATGGTGACACAGAACTGCT+GGG 0.607777 1.4:+55279756 None:intergenic
AGTTTCTTCTCAACCCAACA+AGG 0.609680 1.4:-55280369 MS.gene034536:CDS
AATAACAATGCTGAATATGG+AGG 0.617867 1.4:-55279711 MS.gene034536:CDS
AACCAAACTTCAACTTGACG+AGG 0.618703 1.4:+55279409 None:intergenic
ATGGTGACACAGAACTGCTG+GGG 0.640069 1.4:+55279757 None:intergenic
ACGACCGAAGACGTCGACGA+CGG 0.675975 1.4:-55279795 MS.gene034536:CDS
TGGTGACACAGAACTGCTGG+GGG 0.743324 1.4:+55279758 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTAAATAAGAAATTTAC+AGG + chr1.4:55280298-55280317 None:intergenic 10.0%
!! AAATATATAAAACCATTTAG+AGG + chr1.4:55279659-55279678 None:intergenic 15.0%
!!! TGAAATGTCAATTTTTTTAA+CGG - chr1.4:55279856-55279875 MS.gene034536:intron 15.0%
!!! TTGTTTCTTCTTTTTAATTA+AGG - chr1.4:55280330-55280349 MS.gene034536:CDS 15.0%
!! ATAGTAGATAGAAAATTACA+TGG + chr1.4:55279622-55279641 None:intergenic 20.0%
!!! TTTTTGTTTTTGTTATCATC+AGG - chr1.4:55279983-55280002 MS.gene034536:intron 20.0%
! AGATAGAAAATTACATGGTT+GGG + chr1.4:55279617-55279636 None:intergenic 25.0%
! TAGATAGAAAATTACATGGT+TGG + chr1.4:55279618-55279637 None:intergenic 25.0%
!! AGAAAAGAGATAGGTAATTT+TGG + chr1.4:55279424-55279443 None:intergenic 25.0%
!! ATCATTTTCTTTCCTCTAAA+TGG - chr1.4:55279644-55279663 MS.gene034536:CDS 25.0%
!! TTAAAGTGCTTGAAAATTGT+GGG - chr1.4:55279759-55279778 MS.gene034536:CDS 25.0%
!! TTTAAAGTGCTTGAAAATTG+TGG - chr1.4:55279758-55279777 MS.gene034536:CDS 25.0%
!!! TCAATTTTTTTAACGGATCT+AGG - chr1.4:55279863-55279882 MS.gene034536:intron 25.0%
AAAACCTTGAACCAAATCTT+GGG + chr1.4:55279797-55279816 None:intergenic 30.0%
AAAGCTTCAGAAGAAAAAAG+AGG - chr1.4:55279496-55279515 MS.gene034536:intron 30.0%
AATAACAATGCTGAATATGG+AGG - chr1.4:55280130-55280149 MS.gene034536:intron 30.0%
AGAAACAAGAGAGAAAATGA+AGG - chr1.4:55280154-55280173 MS.gene034536:intron 30.0%
AGGAATAACAATGCTGAATA+TGG - chr1.4:55280127-55280146 MS.gene034536:intron 30.0%
ATACTGAAATCCATTGCAAA+TGG + chr1.4:55280106-55280125 None:intergenic 30.0%
GAAATTTACAGGATTAAGAG+TGG + chr1.4:55280287-55280306 None:intergenic 30.0%
! GAAGTGATGATGATGAAAAT+GGG - chr1.4:55280191-55280210 MS.gene034536:intron 30.0%
!!! TTGTTTTTGTTATCATCAGG+TGG - chr1.4:55279986-55280005 MS.gene034536:intron 30.0%
ATGATGAAAATGGGTCAACT+AGG - chr1.4:55280200-55280219 MS.gene034536:intron 35.0%
CAAAACCTTGAACCAAATCT+TGG + chr1.4:55279798-55279817 None:intergenic 35.0%
GGTTTGTCAAGAAAAGAGAT+AGG + chr1.4:55279433-55279452 None:intergenic 35.0%
TTGAATTTGCACCCAAGATT+TGG - chr1.4:55279783-55279802 MS.gene034536:CDS 35.0%
! GGAAGTGATGATGATGAAAA+TGG - chr1.4:55280190-55280209 MS.gene034536:intron 35.0%
! TTGCAATGGATTTCAGTATG+AGG - chr1.4:55280107-55280126 MS.gene034536:intron 35.0%
!!! TTCTGAAGCTTTTCCTTGTT+GGG + chr1.4:55279488-55279507 None:intergenic 35.0%
AACCAAACTTCAACTTGACG+AGG + chr1.4:55280435-55280454 None:intergenic 40.0%
AATGAAGGTGAAGCTGAAAG+AGG - chr1.4:55280169-55280188 MS.gene034536:intron 40.0%
AGAAGGTCTAGTTGAATAGG+TGG + chr1.4:55279532-55279551 None:intergenic 40.0%
AGTTTCTTCTCAACCCAACA+AGG - chr1.4:55279472-55279491 MS.gene034536:intron 40.0%
GATCTAAGAACAGGAGAGAA+AGG + chr1.4:55279556-55279575 None:intergenic 40.0%
GGAAGAAGGTCTAGTTGAAT+AGG + chr1.4:55279535-55279554 None:intergenic 40.0%
GTAGAAGCAAAAACTTGCAC+TGG - chr1.4:55280389-55280408 MS.gene034536:CDS 40.0%
GTTGAGAAGAAACTTGGTAG+TGG + chr1.4:55279466-55279485 None:intergenic 40.0%
TTCTGTGTCACCATTTGCAA+TGG - chr1.4:55280093-55280112 MS.gene034536:intron 40.0%
! ATGGAACTTGCTTTGAGCTT+AGG - chr1.4:55279391-55279410 MS.gene034536:CDS 40.0%
! TTTGTTATCATCAGGTGGAC+CGG - chr1.4:55279991-55280010 MS.gene034536:intron 40.0%
!! ACTTGGTAGTGGATCTTTGT+TGG + chr1.4:55279455-55279474 None:intergenic 40.0%
!! CTTGGTAGTGGATCTTTGTT+GGG + chr1.4:55279454-55279473 None:intergenic 40.0%
!! TGTTGGGTTGAGAAGAAACT+TGG + chr1.4:55279472-55279491 None:intergenic 40.0%
!!! CTTCTGAAGCTTTTCCTTGT+TGG + chr1.4:55279489-55279508 None:intergenic 40.0%
AAATGGTGACACAGAACTGC+TGG + chr1.4:55280089-55280108 None:intergenic 45.0%
AATGGTGACACAGAACTGCT+GGG + chr1.4:55280088-55280107 None:intergenic 45.0%
GAACAGGAGAGAAAGGAAGA+AGG + chr1.4:55279549-55279568 None:intergenic 45.0%
! TGCACCCAAGATTTGGTTCA+AGG - chr1.4:55279790-55279809 MS.gene034536:CDS 45.0%
!! GTCCTCGTCAAGTTGAAGTT+TGG - chr1.4:55280430-55280449 MS.gene034536:CDS 45.0%
ATGGTGACACAGAACTGCTG+GGG + chr1.4:55280087-55280106 None:intergenic 50.0%
GAATGGGGAGGTGAGAAGAA+GGG + chr1.4:55279585-55279604 None:intergenic 50.0%
GGGTGAGGAGATCTAAGAAC+AGG + chr1.4:55279565-55279584 None:intergenic 50.0%
TTACATGGTTGGGTGAGCCA+AGG + chr1.4:55279607-55279626 None:intergenic 50.0%
! GCTAGACGTGAACCGTTTTC+CGG - chr1.4:55280021-55280040 MS.gene034536:intron 50.0%
ACTGCTGGGGGATGACAATG+AGG + chr1.4:55280074-55280093 None:intergenic 55.0%
ATCATCAGGTGGACCGGTGA+GGG - chr1.4:55279997-55280016 MS.gene034536:intron 55.0%
CTTCTCACCTCCCCATTCCT+TGG - chr1.4:55279587-55279606 MS.gene034536:CDS 55.0%
GGAATGGGGAGGTGAGAAGA+AGG + chr1.4:55279586-55279605 None:intergenic 55.0%
GGTTGGGTGAGCCAAGGAAT+GGG + chr1.4:55279601-55279620 None:intergenic 55.0%
GTTGGGTGAGCCAAGGAATG+GGG + chr1.4:55279600-55279619 None:intergenic 55.0%
TATCATCAGGTGGACCGGTG+AGG - chr1.4:55279996-55280015 MS.gene034536:intron 55.0%
TGGTGACACAGAACTGCTGG+GGG + chr1.4:55280086-55280105 None:intergenic 55.0%
TGGTTGGGTGAGCCAAGGAA+TGG + chr1.4:55279602-55279621 None:intergenic 55.0%
! TTCACGTCTAGCTCCCTCAC+CGG + chr1.4:55280013-55280032 None:intergenic 55.0%
ACGACCGAAGACGTCGACGA+CGG - chr1.4:55280046-55280065 MS.gene034536:intron 60.0%
CTTCGGTCGTCGCCGGAAAA+CGG + chr1.4:55280036-55280055 None:intergenic 60.0%
GGGAGGTGAGAAGAAGGGTG+AGG + chr1.4:55279580-55279599 None:intergenic 60.0%
GGTACCGTCGTCGACGTCTT+CGG + chr1.4:55280053-55280072 None:intergenic 60.0%
GGGTGAGCCAAGGAATGGGG+AGG + chr1.4:55279597-55279616 None:intergenic 65.0%
TCGACGTCTTCGGTCGTCGC+CGG + chr1.4:55280043-55280062 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 55279391 55280472 55279391 ID=MS.gene034536
chr1.4 mRNA 55279391 55280472 55279391 ID=MS.gene034536.t1;Parent=MS.gene034536
chr1.4 exon 55280299 55280472 55280299 ID=MS.gene034536.t1.exon1;Parent=MS.gene034536.t1
chr1.4 CDS 55280299 55280472 55280299 ID=cds.MS.gene034536.t1;Parent=MS.gene034536.t1
chr1.4 exon 55279566 55279841 55279566 ID=MS.gene034536.t1.exon2;Parent=MS.gene034536.t1
chr1.4 CDS 55279566 55279841 55279566 ID=cds.MS.gene034536.t1;Parent=MS.gene034536.t1
chr1.4 exon 55279391 55279470 55279391 ID=MS.gene034536.t1.exon3;Parent=MS.gene034536.t1
chr1.4 CDS 55279391 55279470 55279391 ID=cds.MS.gene034536.t1;Parent=MS.gene034536.t1
Gene Sequence

>MS.gene034536

ATGGAACTTGCTTTGAGCTTAGGTGACACACCAAAATTACCTATCTCTTTTCTTGACAAACCCAACAAAGATCCACTACCAAGTTTCTTCTCAACCCAACAAGGAAAAGCTTCAGAAGAAAAAAGAGGTTCTTCAGATCCACCTATTCAACTAGACCTTCTTCCTTTCTCTCCTGTTCTTAGATCTCCTCACCCTTCTTCTCACCTCCCCATTCCTTGGCTCACCCAACCATGTAATTTTCTATCTACTATAAATCATTTTCTTTCCTCTAAATGGTTTTATATATTTGTTTAATATCTAGATAAATTTGTTTAATTTTATTTTGTTTTTATAGATTTAATTTTATCTTTTTTGTTTTTTTTTTTGTTTTAAAGTGCTTGAAAATTGTGGGTTTGAATTTGCACCCAAGATTTGGTTCAAGGTTTTGCATATTCTTGACTAATGCTTATTGAAAAATATTTGTTATGAAATGTCAATTTTTTTAACGGATCTAGGTTACTTCGAGATATTAGTCTTTGCAGTTACGCGCATGAATTCATATTGTTATAAAAAAAAATTGAAAATATATTTAAAGTTGTATATACTCAATCATTTTTTGTTTTTGTTATCATCAGGTGGACCGGTGAGGGAGCTAGACGTGAACCGTTTTCCGGCGACGACCGAAGACGTCGACGACGGTACCTCATTGTCATCCCCCAGCAGTTCTGTGTCACCATTTGCAATGGATTTCAGTATGAGGAATAACAATGCTGAATATGGAGGAAGAAACAAGAGAGAAAATGAAGGTGAAGCTGAAAGAGGAAGTGATGATGATGAAAATGGGTCAACTAGGAAGAAACTAAGACTCTCTAAAGATCAATCTGCTTTTCTTGAAGAAAGTTTCAAAGAACACACCACTCTTAATCCTGTAAATTTCTTATTTAATTTTTGTTTATTTACTTGTTTCTTCTTTTTAATTAAGGTTTATTTGTTAATTAATCATGTTTATTTATTTGCTTGTAGAAGCAAAAACTTGCACTGGCAAAACAGTTGAATCTTAGTCCTCGTCAAGTTGAAGTTTGGTTTCAAAATAGAAGAGCAAG
Protein sequence

>MS.gene034536.t1

MELALSLGDTPKLPISFLDKPNKDPLPSFFSTQQGKASEEKRGSSDPPIQLDLLPFSPLDVNRFPATTEDVDDGTSLSSPSSSVSPFAMDFSMRNNNAEYGGRNKRENEGEAERGSDDDENGSTRKKLRLSKDQSAFLEESFKEHTTLNPKQKLALAKQLNLSPRQVEVWFQNRRA